Extensive direct-tandem organization of a long repeat DNA sequence on the Y chromosome of chinook salmon (Oncorhynchus tshawytscha)

A long repetitive DNA sequence (OtY8) has been cloned from male chinook salmon and its genomic organization has been characterized. The repeat has a unit length of 8 kb and is present approximately 300 times per diploid male nucleus. All internal fragments within the 8-kb repeat segregate from father to son, suggesting that the entire repeat unit is located on the Y chromosome. The organization of this sequence into an 8-kb repeat unit is restricted to the Y chromosome, as are several male-specific repeat subtypes identified on the basis of restriction-site variation. The repeat possesses only weak internal sequence similarities, suggesting that OtY8 has not arisen by duplication of a smaller repeat unit, as is the case for other long tandem arrays found in eukaryotes. Based on a laddered pattern arising from partial digestion of genomic DNA with a restriction enzyme which cuts only once per repeat unit, this sequence is not dispersed on the Y chromosome but is organized as a head-to-tail tandem array. Pulse-gel electrophoresis reveals that the direct-tandem repeats are organized into at least six separate clusters containing approximately 12 to 250 copies, comprising some 2.4 Mb of Y-chromosomal DNA in total. Related sequences with nucleotide substitutions and DNA insertions relative to the Y-chromosomal fragment are found elsewhere in the genome but at much lower copy number and, although similar sequences are also found in other salmonid species, the amplification of the repeat into a Y-chromosome-linked tandem array is only observed in chinook salmon. The OtY8 repetitive sequence is genetically tightly associated with the sex-determination locus and provides an opportunity to examine the evolution of the Y chromosome and sex determination process in a lower vertebrate.     

Defining the outcome of immunosuppression withdrawal after liver transplantation

Successful immunosuppression withdrawal should benefit the natural history of organ transplantation patients. To identify the clinical hazards of removing drug treatment and possible characteristics that predict a favorable outcome in long-term liver recipients, immunosuppression was withdrawn completely and the clinicopathological outcome documented in 18 liver recipients. Indication for transplantation, HLA matching, early rejection history, and presence of microchimerism were examined as predictors of outcome. Chimerism was determined by polymerase chain reaction-based examination for donor-specific HLA-DRB1 alleles and Y-gene-specific nucleotide sequences. At 3 years, 5 patients (28%) remained completely off immunosuppression; 12 patients (67%) experienced histological graft changes: acute rejection in 4, portal tract inflammation/hepatitis in 7, and necrosis in 1. Hepatitis B or C viral infections did not account for the nonrejection patterns. Unmasking of systemic disorders occurred. Chimerism, demonstrated in 7 patients (39%), with skin the optimal tissue, was not associated with tolerance. Parameters associated with successful drug withdrawal were transplantation for non-immune-mediated liver disorders, fewer donor-recipient HLA A, B, and DR mismatches, and a low incidence of early rejection. Immunosuppression withdrawal is a feasible option in a proportion of selected liver recipients, but identification of tolerant patients remains imprecise.     

Bacteria for the nineties

Staphylococcus aureus and Enterococci have gained prominence as the causes of wound infections during this decade. Methicillin-resistant Staphylococcus aureus (MRSA) became commonplace in the United States during the 1980s. In Canada, infections with MRSA have been increasing in frequency since 1995. MRSA develops resistance by producing an altered penicillin-binding protein, PBP 2a, coded for by the mecA gene. Vancomycin is the usual drug of choice. Recently, strains with intermediate resistance to vancomycin (VISA) have been isolated from patients in Japan and the United States. Interim guidelines for their control have been developed by the Centers for Disease Control. Enterococci have developed a resistance to a variety of antimicrobials during the past three decades, including beta-lactams and aminoglycosides. Recently, strains resistant to vancomycin (VRE) have been found in the United States and Canada. They are particularly difficult to treat, although some success has been achieved with experimental drugs. These microorganisms have the ability to escape control by antimicrobials almost as soon as they are developed. Thus, we must practice good infection control and reserve antimicrobials only for clear cases of infection if we are to prevent or delay the emergence of resistance.     

Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock

Circadian clocks are synchronized by environmental cues such as light. Photoreceptor-deficient Arabidopsis thaliana mutants were used to measure the effect of light fluence rate on circadian period in plants. Phytochrome B is the primary high-intensity red light photoreceptor for circadian control, and phytochrome A acts under low-intensity red light. Cryptochrome 1 and phytochrome A both act to transmit low-fluence blue light to the clock. Cryptochrome 1 mediates high-intensity blue light signals for period length control. The presence of cryptochromes in both plants and animals suggests that circadian input pathways have been conserved throughout evolution.     

A 3-degree of freedom binary search pose estimation technique

This paper describes a novel, binary search pose estimation (BSPE) technique for poses constrained to 3 degrees of freedom (DOF). The technique requires three fiduciary marker points and operates by minimising the angular DOF through a binary search driven algorithm. The technique is less computationally intensive than the standard closed form solutions and quickly converges to a solution which can be verified if additional fiduciary points are available. Evaluation for the technique is presented through a comparison to pose from orthography and scaling with iterations (POSIT) using synthetic data and a real-world application, where the technique is used for pose estimation of a mobile robot with respect to a motor vehicle for inspection purposes.     

Growth and feeding efficiency of wild and aquaculture genotypes of rainbow trout (Oncorhynchus mykiss) common to Lake Huron,Canada

Selective breeding of salmonid fishes for the purpose of commercial aquaculture has resulted in domesticated strains possessing a divergent physiological and behavioral phenotype from that of wild conspecifics. Freshwater production of rainbow trout (Oncorhynchus mykiss) has been occurring in regions of Lake Huron, Canada, for decades yet the growth and performance of domestic (aquaculture) versus wild (naturalized) strains are poorly understood. We conducted two trials to examine growth differences between size-matched wild and domestic strains of juvenile rainbow trout: (1) reared separately and fed to satiation; and (2) reared together and fed a reduced ration to induce competition. Additionally, we used bioenergetics models to assess strain-specific growth rates across a range of water temperatures (5, 10, 15 and 18 °C) as well as Lake Huron temperatures during the open-water season. Domestic rainbow trout showed a growth advantage throughout the 102 d trials, and by the end of the study had achieved a mass > two-fold that of the wild strain and had greater fork length, condition, and thermal growth coefficient (TGC) under both treatments. Rapid growth of domestic strain fish was achieved through the combination of enhanced feed consumption (by ~ 40%) and feeding efficiency (up to 60% lower feed conversion ratio) relative to wild fish. Divergence in growth rates between strains was most pronounced (> 3 ×) when modeled with Lake Huron open-water temperatures. We demonstrate that the growth and feed-conversion efficiency differ significantly between these two strains of rainbow trout under laboratory conditions, suggesting that differences could be even greater in nature.     

An economic assessment of potential ethanol production pathways in Ireland

An economic assessment was conducted on five biomass-to-ethanol production pathways utilising the feedstock: wheat, triticale, sugarbeet, miscanthus and straw. The analysis includes the costs and margins for all the stakeholders along the economic chain. This analysis reveals that under current market situations in Ireland, the production of ethanol under the same tax regime as petrol makes it difficult to compete against that fuel, with tax breaks, however, it can compete against petrol. On the other hand, even under favourable tax breaks it will be difficult for indigenously produced ethanol to compete against cheaper sources of imported ethanol. Therefore, the current transport fuel market has no economic reason to consume indigenously produced ethanol made from the indigenously grown feedstock analysed at a price that reflects all the stakeholders’ costs. To deliver a significant penetration of indigenous ethanol into the market would require some form of compulsory inclusion or else considerable financial supports to feedstock and ethanol producers.